RetrogeneDB ID: retro_ptro_828

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:59962601..59963412(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TARDBP
• Ensembl ID: ENSPTRG00000000136
• Aliases: None
• Description: None

Sequence

>retro_ptro_828
ATATCTGAATATATTCGCGTACCGAAGATGAGAAGGATGAGCCCATTGAAATACCATCGGAAGACGATGGGATGGTGCTG
CTGTCCATGGTTACAGCCCAGTTTCCAGGGGTGTGTGGGCTTCGCTACAGAAATCCAGTGTCTCAGTGTATGAGAGGTGT
CCGGCTGGTAGAAGGAATTCTTCATGCCCCCAATTCTGGCTGGGAAATCTGGTGTATGTTGTCAACTATCCTAAAGATAA
CAAAAGAAAAATGGATGAGATAGATGCTTCATCAGCTGTGAAAGTGAAAAGAGCAGTCCAGAAAACATCTGATTTAGTAG
TGTTGGGTCTCACATGGAAAACAACTGAGCAGGACCTGAAAGAATATTTTAGTACCTTTGGAGAAGTTCTTATGGTGCAG
GTCAAGAAAGATACTAAGACTGGTCATTCAAAGAGGTTTGGCTTCATTTGTTTTATGGAAGATGAAACACAGGTGAAAGT
AATGTCACAGCTACATATGATAGATGGACGATGGTGTGACTGTAAACTTCCCAATTCTAAGCAAAGCCCAGATAAGCCTT
TGAGAAGCATGAAAGTGTTTGTGGGGCGCTGAACAGAGGACATGACTGCGGATGAGCTGCGGCAGTTCTTCTGTCAGTAC
GGGGAAGTGGTGGATGTCGTCATCCTCAAGCCATTCAGGACGTTTGCCTTTGTTACATTTGCAGATGATCAGGTTGCGCA
GTCTTTTTGTGGAGAGGACTTGATCATTAAAGGAATCAGCATTCATATATCCAATGCCGAACCTAAGCACAACAGCAATA
GACAGAAAGAA

Alignment

ORF - retro_ptro_828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.18 %
• Parental protein coverage: 65.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEYIRV-TEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGW-
          .SEYIRV.TEDE.DEPIEIPSEDDG.VLLS.VTAQFPG.CGLRYRNPVSQCMRGVRLVEGILHAP..GW.
Retrocopy ISEYIRV<TEDEKDEPIEIPSEDDGMVLLSMVTAQFPGVCGLRYRNPVSQCMRGVRLVEGILHAPNSGW<

Parental  GNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD
          GNLVYVVNYPKDNKRKMDE.DASSAVKVKRAVQKTSDL.VLGL.WKTTEQDLKEYFSTFGEVLMVQVKKD
Retrocopy GNLVYVVNYPKDNKRKMDEIDASSAVKVKRAVQKTSDLVVLGLTWKTTEQDLKEYFSTFGEVLMVQVKKD

Parental  LKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDELR
          .KTGHSK.FGF..F.E.ETQVKVMSQ.HMIDGRWCDCKLPNSKQS.D.PLRS.KVFVGR.TEDMT.DELR
Retrocopy TKTGHSKRFGFICFMEDETQVKVMSQLHMIDGRWCDCKLPNSKQSPDKPLRSMKVFVGR*TEDMTADELR

Parental  EFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNRQLE
          .FF.QYG.V.DV.I.KPFR.FAFVTFADDQ.AQS.CGEDLIIKGIS.HISNAEPKHNSNRQ.E
Retrocopy QFFCQYGEVVDVVILKPFRTFAFVTFADDQVAQSFCGEDLIIKGISIHISNAEPKHNSNRQKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	107.44 RPM
SRP007412_cerebellum	0.00 RPM	197.99 RPM
SRP007412_heart	0.00 RPM	100.03 RPM
SRP007412_kidney	0.05 RPM	120.64 RPM
SRP007412_liver	0.00 RPM	95.62 RPM
SRP007412_testis	0.00 RPM	160.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_828 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_828 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1209
Pongo abelii	retro_pabe_1008

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460, retro_ptro_828 ,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,